While early gut microbial dynamics and their links to paediatric health have been considerably studied, the bacterial colonisation of the early infant respiratory system remains poorly understood, par

The gap

Consensus across the literature

Supporting evidence — 4 representative gaps

• Early-life Gut Microbiota and Allergic Diseases: Immune Regulatory Mechanisms and Intervention Progress (2026) · doi

  The early-life gut microbiota develops in parallel with the immune system and may contribute to the development and progression of allergic diseases by regulating immune tol- erance, epithelial barrier function, Th2-type immune skew- ing, and cross-organ immune communication through the gut–skin and gut–lung axes. Current evidence indicates that alterations in gut microbiota composition, diversity, maturation trajectories, and metabolic function during early life are associated with the risk of allergic diseases. Microbiota-targeted strategies, including probiotics, prebi- otics, dietary interventions, FMT, and maternal microbial seeding, provide new directions for the prevention and intervention of allergic diseases. Before these findings can be translated into routine clinical practice, several challenges need to be addressed. First, human longitudinal cohorts mainly provide temporal associations, and the causal relationship between early life dysbiosis and allergic disease development remains to be confirmed. Second, current mechanistic studies on how the early life gut microbiota regulates immune development and allergic susceptibility are largely derived from ani- mal models and still require validation in human infants. Future studies should establish standardized, deeply phe- notyped, and long-term birth cohorts that integrate micro- biota, metabolomic, immune phenotyping, environmental exposure, and clinical outcome data. In combination with single-cell multi-omics, spatial transcriptomics, organ- oids, and ex vivo immune models, these studies may help clarify key mechanisms, reproducible biomarkers, and optimal intervention windows. Well-designed clini- cal trials are also needed to evaluate the safety, durability of efficacy, and target populations of microbiota-targeted interventions, thereby promoting the translation of mecha- nistic insights into precision prevention and clinical prac- tice (Table 1). 1 3Clinical Reviews in Allergy & Immunology (2026) 69:49 Table 1 Early-life gut microbiota and allergic diseases: challenges, gaps, and future directions

  Keywords: immune microbiota allergic early life diseases clinical development function organ current targeted interventions provide directions
• Strain-level microbial signatures and inferred functional alterations in infants with food protein-induced allergic proctocolitis (2026) · doi

  This work generates several hypotheses for future study regarding potential early microbial biomarkers and novel interventional targets for AP, which also represents an understudied opportunity for life-threatening IgE-medi- ated food allergy prevention.

  Keywords: generates several hypotheses future regarding potential early microbial biomarkers novel interventional targets represents understudied opportunity
• Gastrointestinal disorders associated with gut microbiota dysbiosis in children aged 0–3 years (2026) · doi

  Further research on the gut microbiota in early child- hood is essential to better understand its role in the de- velopment of chronic conditions such as allergies, autoimmune diseases, obesity, and metabolic disorders. Although the current evidence shows a strong link between dysbiosis and various health problems in children, the underlying mechanisms remain in- completely understood. Future studies should analyze in detail how the gut microbiota influences immune system development, gastrointestinal maturation, and its interactions with environmental and genetic factors. In addition, developing more precise and ac- cessible diagnostic tools, including microbiota pro- filing tests, will enable earlier detection and more effective treatment approaches. A deeper understanding of how the gut microbiome shapes long-term health has the potential to transform preventive and therapeutic strategies for chronic diseases – particularly in children – and may serve as a cornerstone for future public health interventions. Authors’ contribution Study design – A. Kwiatkowski, M. Kleinert Data collection – A. Kwiatkowski, T. Lepich Manuscript preparation – A. Kwiatkowski, J. Kwiatkowska Literature research – A. Kwiatkowski, M. Górski, R. Polaniak Final approval of the version to be published – A. Kwiatkowski, M. Kleinert, T. Lepich, M. Górski, J. Kwiatkowska, R. Polaniak REFERENCES and Rev.

  Keywords: kwiatkowski microbiota health chronic diseases children future kleinert lepich kwiatkowska rski polaniak further early child
• Bacterial diversity and strain dynamics in the infant respiratory microbiome during the first year of life (2026) · doi

  While early gut microbial dynamics and their links to paediatric health have been considerably studied, the bacterial colonisation of the early infant respiratory system remains poorly understood, particularly at the species and strain level.

  Keywords: early microbial dynamics links paediatric health considerably studied bacterial colonisation infant respiratory system remains poorly